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Detailed information for vg1109266463:

Variant ID: vg1109266463 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9266463
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAAGTTGTTATCCAAATTTTGGAAGTTTTTGTCCTAGGGGTATTTCGGTCATTTGGACAAAATTGTACAGTACTAACGGAGGCTAACCGGACGGCGAT[G/A]
GTAAATCGTAGAAGTTAAGCAAAAGTCGATGGTATATTGTAGATCGTGATAAAGTCGATGATAAATCGTAGACATGTGACAAAGTCAGTGGCATATAATG

Reverse complement sequence

CATTATATGCCACTGACTTTGTCACATGTCTACGATTTATCATCGACTTTATCACGATCTACAATATACCATCGACTTTTGCTTAACTTCTACGATTTAC[C/T]
ATCGCCGTCCGGTTAGCCTCCGTTAGTACTGTACAATTTTGTCCAAATGACCGAAATACCCCTAGGACAAAAACTTCCAAAATTTGGATAACAACTTCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	12.50%	0.23%	35.76%	NA
All Indica	2759	20.30%	20.00%	0.40%	59.26%	NA
All Japonica	1512	97.60%	0.10%	0.00%	2.25%	NA
Aus	269	93.70%	5.90%	0.00%	0.37%	NA
Indica I	595	24.00%	0.50%	0.67%	74.79%	NA
Indica II	465	8.80%	54.00%	0.22%	36.99%	NA
Indica III	913	20.60%	15.40%	0.11%	63.86%	NA
Indica Intermediate	786	23.90%	20.10%	0.64%	55.34%	NA
Temperate Japonica	767	97.40%	0.10%	0.00%	2.48%	NA
Tropical Japonica	504	97.40%	0.20%	0.00%	2.38%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	57.80%	21.10%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109266463	G -> A	LOC_Os11g16720.1	downstream_gene_variant ; 1339.0bp to feature; MODIFIER	silent_mutation	Average:17.928; most accessible tissue: Callus, score: 38.225	N	N	N	N
vg1109266463	G -> A	LOC_Os11g16730.1	downstream_gene_variant ; 180.0bp to feature; MODIFIER	silent_mutation	Average:17.928; most accessible tissue: Callus, score: 38.225	N	N	N	N
vg1109266463	G -> A	LOC_Os11g16720-LOC_Os11g16730	intergenic_region ; MODIFIER	silent_mutation	Average:17.928; most accessible tissue: Callus, score: 38.225	N	N	N	N
vg1109266463	G -> DEL	N	N	silent_mutation	Average:17.928; most accessible tissue: Callus, score: 38.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109266463	NA	3.03E-06	mr1892	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1109266463	NA	3.91E-06	mr1361_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251